scholarly journals The stress-sensing domain of activated IRE1α forms helical filaments in narrow ER membrane tubes

2021 ◽  
Author(s):  
Stephen D. Carter ◽  
Ngoc-Han Tran ◽  
Ann De Mazière ◽  
Avi Ashkenazi ◽  
Judith Klumperman ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Light And Electron Microscopy ◽  
Unfolded Protein ◽  
Left Handed ◽  
Stress Sensing ◽  
The Unfolded Protein Response ◽  
Protein Response ◽  
Lumenal Domain ◽  
Er Membrane

The signaling network of the unfolded protein response (UPR) adjusts the protein folding capacity of the endoplasmic reticulum (ER) according to need. The most conserved UPR sensor, IRE1α, spans the ER membrane and activates through oligomerization. IRE1α oligomers accumulate in dynamic foci. We determined the in-situ structure of IRE1α foci by cryogenic correlated light and electron microscopy (cryo-CLEM), combined with electron cryo-tomography (cryo-ET) and complementary immuno-electron microscopy. IRE1α oligomers localize to a network of narrow anastomosing ER tubes (diameter ~28 nm) with complex branching. The lumen of the tubes contains protein filaments, likely composed of linear arrays of IRE1α lumenal domain dimers, arranged in two intertwined, left-handed helices. Our findings define a previously unrecognized ER subdomain and suggest positive feedback in IRE1 signaling.

scholarly journals An unfolded protein-induced conformational switch activates mammalian IRE1

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
G Elif Karagöz ◽  
Diego Acosta-Alvear ◽  
Hieu T Nguyen ◽  
Crystal P Lee ◽  
Feixia Chu ◽  
...  
Keyword(s):  
Peptide Binding ◽  
Common Mechanism ◽  
Unfolded Proteins ◽  
Conformational Switch ◽  
Allosteric Coupling ◽  
Unfolded Protein ◽  
Stress Sensing ◽  
The Unfolded Protein Response ◽  
Protein Response ◽  
Lumenal Domain

The unfolded protein response (UPR) adjusts the cell’s protein folding capacity in the endoplasmic reticulum (ER) according to need. IRE1 is the most conserved UPR sensor in eukaryotic cells. It has remained controversial, however, whether mammalian and yeast IRE1 use a common mechanism for ER stress sensing. Here, we show that similar to yeast, human IRE1α’s ER-lumenal domain (hIRE1α LD) binds peptides with a characteristic amino acid bias. Peptides and unfolded proteins bind to hIRE1α LD’s MHC-like groove and induce allosteric changes that lead to its oligomerization. Mutation of a hydrophobic patch at the oligomerization interface decoupled peptide binding to hIRE1α LD from its oligomerization, yet retained peptide-induced allosteric coupling within the domain. Importantly, impairing oligomerization of hIRE1α LD abolished IRE1’s activity in living cells. Our results provide evidence for a unifying mechanism of IRE1 activation that relies on unfolded protein binding-induced oligomerization.

scholarly journals The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasis

eLife ◽  
2012 ◽  
Vol 1 ◽  
Author(s):  
Philipp Kimmig ◽  
Marcy Diaz ◽  
Jiashun Zheng ◽  
Christopher C Williams ◽  
Alexander Lang ◽  
...  
Keyword(s):  
Er Stress ◽  
Fission Yeast ◽  
Unfolded Protein Response ◽  
Unfolded Protein ◽  
Er Chaperone ◽  
Stress Sensing ◽  
Transcription Activators ◽  
The Unfolded Protein Response ◽  
Protein Response ◽  
Selective Decay

The unfolded protein response (UPR) monitors the protein folding capacity of the endoplasmic reticulum (ER). In all organisms analyzed to date, the UPR drives transcriptional programs that allow cells to cope with ER stress. The non-conventional splicing of Hac1 (yeasts) and XBP1 (metazoans) mRNA, encoding orthologous UPR transcription activators, is conserved and dependent on Ire1, an ER membrane-resident kinase/endoribonuclease. We found that the fission yeast Schizosaccharomyces pombe lacks both a Hac1/XBP1 ortholog and a UPR-dependent-transcriptional-program. Instead, Ire1 initiates the selective decay of a subset of ER-localized-mRNAs that is required to survive ER stress. We identified Bip1 mRNA, encoding a major ER-chaperone, as the sole mRNA cleaved upon Ire1 activation that escapes decay. Instead, truncation of its 3′ UTR, including loss of its polyA tail, stabilized Bip1 mRNA, resulting in increased Bip1 translation. Thus, S. pombe uses a universally conserved stress-sensing machinery in novel ways to maintain homeostasis in the ER.

scholarly journals Caspase-mediated cleavage of IRE1 controls apoptotic cell commitment during endoplasmic reticulum stress

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Anna Shemorry ◽  
Jonathan M Harnoss ◽  
Ofer Guttman ◽  
Scot A Marsters ◽  
László G Kőműves ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Er Stress ◽  
Apoptotic Cell ◽  
Leukemia Cell ◽  
Unfolded Protein ◽  
Proapoptotic Protein ◽  
Stress Sensing ◽  
The Unfolded Protein Response ◽  
Cell Commitment ◽  
Protein Response

Upon detecting endoplasmic reticulum (ER) stress, the unfolded protein response (UPR) orchestrates adaptive cellular changes to reestablish homeostasis. If stress resolution fails, the UPR commits the cell to apoptotic death. Here we show that in hematopoietic cells, including multiple myeloma (MM), lymphoma, and leukemia cell lines, ER stress leads to caspase-mediated cleavage of the key UPR sensor IRE1 within its cytoplasmic linker region, generating a stable IRE1 fragment comprising the ER-lumenal domain and transmembrane segment (LDTM). This cleavage uncouples the stress-sensing and signaling domains of IRE1, attenuating its activation upon ER perturbation. Surprisingly, LDTM exerts negative feedback over apoptotic signaling by inhibiting recruitment of the key proapoptotic protein BAX to mitochondria. Furthermore, ectopic LDTM expression enhances xenograft growth of MM tumors in mice. These results uncover an unexpected mechanism of cross-regulation between the apoptotic caspase machinery and the UPR, which has biologically significant consequences for cell survival under ER stress.

scholarly journals Activation of the IRE1 RNase through remodeling of the kinase front pocket by ATP-competitive ligands

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Elena Ferri ◽  
Adrien Le Thomas ◽  
Heidi Ackerly Wallweber ◽  
Eric S. Day ◽  
Benjamin T. Walters ◽  
...  
Keyword(s):  
Small Molecule ◽  
Kinase Inhibitors ◽  
Endoplasmic Reticulum Membrane ◽  
Cellular Activity ◽  
Unfolded Proteins ◽  
Unfolded Protein ◽  
Dimeric Unit ◽  
The Unfolded Protein Response ◽  
Protein Response ◽  
Lumenal Domain

AbstractInositol-Requiring Enzyme 1 (IRE1) is an essential component of the Unfolded Protein Response. IRE1 spans the endoplasmic reticulum membrane, comprising a sensory lumenal domain, and tandem kinase and endoribonuclease (RNase) cytoplasmic domains. Excess unfolded proteins in the ER lumen induce dimerization and oligomerization of IRE1, triggering kinase trans-autophosphorylation and RNase activation. Known ATP-competitive small-molecule IRE1 kinase inhibitors either allosterically disrupt or stabilize the active dimeric unit, accordingly inhibiting or stimulating RNase activity. Previous allosteric RNase activators display poor selectivity and/or weak cellular activity. In this study, we describe a class of ATP-competitive RNase activators possessing high selectivity and strong cellular activity. This class of activators binds IRE1 in the kinase front pocket, leading to a distinct conformation of the activation loop. Our findings reveal exquisitely precise interdomain regulation within IRE1, advancing the mechanistic understanding of this important enzyme and its investigation as a potential small-molecule therapeutic target.

scholarly journals Live imaging of the co-translational recruitment of XBP1 mRNA to the ER and its processing by diffuse, non-polarized IRE1a.

2021 ◽  
Author(s):  
Silvia Gomez-Puerta ◽  
Roberto Ferrero ◽  
Tobias Hochstoeger ◽  
Ivan Zubiri ◽  
Jeffrey A. Chao ◽  
...  
Keyword(s):  
Er Stress ◽  
Single Molecule ◽  
Oligomeric State ◽  
Unfolded Protein ◽  
Xbp1 Mrna ◽  
Imaging Approach ◽  
The Unfolded Protein Response ◽  
Large Clusters ◽  
Protein Response ◽  
Er Membrane

Endoplasmic reticulum (ER) to nucleus homeostatic signalling, known as the unfolded protein response (UPR), relies on the non-canonical splicing of XBP1 mRNA. The molecular switch that initiates splicing is the oligomerization of the ER stress sensor and UPR endonuclease IRE1a. While IRE1a can form large clusters that have been proposed to function as XBP1 processing centers on the ER, the actual oligomeric state of active IRE1a complexes as well as the targeting mechanism that recruits XBP1 to IRE1a oligomers, remain unknown. Here, we used a single molecule imaging approach to directly monitor the recruitment of individual XBP1 transcripts to the ER surface. We confirmed that stable ER association of unspliced XBP1 mRNA is established through HR2-dependent targeting and relies on active translation. In addition, we show that IRE1a-catalyzed splicing mobilizes XBP1 mRNA from the ER membrane in response to ER stress. Surprisingly, we find that XBP1 transcripts are not recruited into large IRE1a clusters, which only assemble upon overexpression of fluorescently-tagged IRE1a during ER stress. Our findings support a model where ribosome-engaged, ER-poised XBP1 mRNA is processed by functional IRE1a assemblies that are homogenously distributed throughout the ER membrane.

scholarly journals How to design an optimal sensor network for the unfolded protein response

2018 ◽  
Vol 29 (25) ◽  
pp. 3052-3062 ◽  
Author(s):  
Wylie Stroberg ◽  
Hadar Aktin ◽  
Yonatan Savir ◽  
Santiago Schnell
Keyword(s):  
Er Stress ◽  
Unfolded Protein Response ◽  
Cellular Protein ◽  
Protein Accumulation ◽  
Protein Homeostasis ◽  
Unfolded Protein ◽  
Stress Sensing ◽  
Coarse Model ◽  
The Unfolded Protein Response ◽  
Protein Response

Cellular protein homeostasis requires continuous monitoring of stress in the endoplasmic reticulum (ER). Stress-detection networks control protein homeostasis by mitigating the deleterious effects of protein accumulation, such as aggregation and misfolding, with precise modulation of chaperone production. Here, we develop a coarse model of the unfolded protein response in yeast and use multi-objective optimization to determine which sensing and activation strategies optimally balance the trade-off between unfolded protein accumulation and chaperone production. By comparing a stress-sensing mechanism that responds directly to the level of unfolded protein in the ER to a mechanism that is negatively regulated by unbound chaperones, we show that chaperone-mediated sensors are more efficient than sensors that detect unfolded proteins directly. This results from the chaperone-mediated sensor having separate thresholds for activation and deactivation. Finally, we demonstrate that a sensor responsive to both unfolded protein and unbound chaperone does not further optimize homeostatic control. Our results suggest a strategy for designing stress sensors and may explain why BiP-mitigated ER stress-sensing networks have evolved.

scholarly journals The Unfolded Protein Response as a Guardian of the Secretory Pathway

Cells ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2965
Author(s):  
Toni Radanović ◽  
Robert Ernst
Keyword(s):  
Protein Folding ◽  
Unfolded Protein Response ◽  
Secretory Pathway ◽  
Unfolded Proteins ◽  
Storage Lipids ◽  
Unfolded Protein ◽  
Membrane Stiffness ◽  
The Unfolded Protein Response ◽  
Protein Response ◽  
Er Membrane

The endoplasmic reticulum (ER) is the major site of membrane biogenesis in most eukaryotic cells. As the entry point to the secretory pathway, it handles more than 10,000 different secretory and membrane proteins. The insertion of proteins into the membrane, their folding, and ER exit are affected by the lipid composition of the ER membrane and its collective membrane stiffness. The ER is also a hotspot of lipid biosynthesis including sterols, glycerophospholipids, ceramides and neural storage lipids. The unfolded protein response (UPR) bears an evolutionary conserved, dual sensitivity to both protein-folding imbalances in the ER lumen and aberrant compositions of the ER membrane, referred to as lipid bilayer stress (LBS). Through transcriptional and non-transcriptional mechanisms, the UPR upregulates the protein folding capacity of the ER and balances the production of proteins and lipids to maintain a functional secretory pathway. In this review, we discuss how UPR transducers sense unfolded proteins and LBS with a particular focus on their role as guardians of the secretory pathway.

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